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4bbbc6611dbe4bf05ed36ea795b3c6dc39bbdebc
rdkit/Code/GraphMol
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Greg Landrum 4bbbc6611d Add a CXSMILES option to the MolHash (#5058) 
* Nonchiral atoms should be removed from StereoGroups

This fixes a bug where atoms which have no chirality were left in StereoGroups

In order to make this work, ROMol::setStereoGroups() needed to be made public.
That shouldn't be a problem since it doesn't change connectivity.

* support CXSmiles extensions in the hashes

* initial tests for that

* some cleanup

* copyright header cleanup

* minor refactoring

* call out the changes in the release notes

* extension and more testing

* add python wrappers
2022-03-03 16:00:38 +01:00
..
Abbreviations
Fix a number of crashing bugs in the python wrappers (#4810)
2021-12-27 16:09:06 -05:00
Basement/FeatTrees
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ChemReactions
Support writing V3000 reactions (#4982)
2022-02-08 14:37:53 +01:00
ChemTransforms
Fixes #4809: double bond stereo can now be set after calling replaceCore() (#4827)
2021-12-29 09:03:09 +01:00
CIPLabeler
Fixes #4996 and #4998 (#5001)
2022-02-12 04:18:17 +01:00
Depictor
Some refactoring of the depictor code (#4865)
2022-01-20 05:20:01 +01:00
Deprotect
Improvements to some constructors in python wrappers (#4581)
2021-10-06 04:17:53 +02:00
Descriptors
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
DistGeomHelpers
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
FileParsers
Refactor mol draw2 d (#4948)
2022-02-18 16:30:21 +01:00
FilterCatalog
Support for logging via Python's logging module. (#4846)
2022-01-24 04:49:27 +01:00
Fingerprints
Fixes #5036 (#5041)
2022-02-23 06:11:40 -05:00
FMCS
Make FMCS check bond stereo. (#5009)
2022-02-22 06:50:17 +01:00
ForceFieldHelpers
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
FragCatalog
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
GenericGroups
Fixes crashing bug with finalSubstructChecks (#4782)
2021-12-10 08:22:59 +01:00
libs
Unset executable flag
2019-10-10 20:18:43 +09:00
MMPA
Fix a number of crashing bugs in the python wrappers (#4810)
2021-12-27 16:09:06 -05:00
MolAlign
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
MolCatalog
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
MolChemicalFeatures
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
MolDraw2D
fix MSVC DLL build after moldraw2d refactor (#5046)
2022-03-02 17:13:32 +01:00
MolEnumerator
Fix some problems turned up by ossfuzz (#4927)
2022-01-22 04:30:06 +01:00
MolHash
Add a CXSMILES option to the MolHash (#5058)
2022-03-03 16:00:38 +01:00
MolInterchange
Fix a number of crashing bugs in the python wrappers (#4810)
2021-12-27 16:09:06 -05:00
MolStandardize
Fix a number of crashing bugs in the python wrappers (#4810)
2021-12-27 16:09:06 -05:00
MolTransforms
cleanup some compiler warnings (#4521)
2021-09-16 04:34:40 +02:00
PartialCharges
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
ReducedGraphs
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
RGroupDecomposition
Refactor mol draw2 d (#4948)
2022-02-18 16:30:21 +01:00
ScaffoldNetwork
Fix a number of crashing bugs in the python wrappers (#4810)
2021-12-27 16:09:06 -05:00
ShapeHelpers
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
SLNParse
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
SmilesParse
Fixes #4981 (#5030)
2022-02-22 20:35:44 +01:00
StructChecker
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Subgraphs
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Substruct
[WIP] Clean up the warning landscape (#5048)
2022-03-01 05:00:25 +01:00
SubstructLibrary
Support for logging via Python's logging module. (#4846)
2022-01-24 04:49:27 +01:00
TautomerQuery
remove dead code (#4739)
2021-11-29 08:00:21 +01:00
test_data
miscellaneous updates (#4284)
2021-07-13 06:57:29 +02:00
testExecs
Unset executable flag
2019-10-10 20:18:43 +09:00
Trajectory
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Wrap
Expose MolzipParams::atomSymbols to python (#5054)
2022-02-28 06:42:52 +01:00
AddHs.cpp
Fix some problems turned up by ossfuzz (#4927)
2022-01-22 04:30:06 +01:00
AdjustQuery.cpp
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
Aromaticity.cpp
Fixes #4721 (#4722)
2022-01-28 16:38:46 +01:00
Atom.cpp
Move isEarlyAtom to a table to reduce lock contention in getPeriodicTable (#4980)
2022-02-03 16:03:17 +01:00
Atom.h
Start adding move constructors and move-assignment operators (#4909)
2022-02-09 14:20:49 +01:00
atomic_data.cpp
Fixes #3531 (#3545)
2020-11-08 07:17:37 +01:00
atomic_data.h
miscellaneous updates (#4284)
2021-07-13 06:57:29 +02:00
AtomIterators.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
AtomIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
Bond.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
Bond.h
Start adding move constructors and move-assignment operators (#4909)
2022-02-09 14:20:49 +01:00
BondIterators.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
BondIterators.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
bulktest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Canon.cpp
Fixes #4582 (#4587)
2021-10-08 05:19:43 +02:00
Canon.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
catch_adjustquery.cpp
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
catch_chirality.cpp
Add a CXSMILES option to the MolHash (#5058)
2022-03-03 16:00:38 +01:00
catch_graphmol.cpp
resolves bad input in one of the tests (#5002)
2022-02-10 08:02:33 +01:00
catch_main.cpp
Fixes #4508 (#4512)
2021-09-15 16:06:36 +02:00
catch_moliterators.cpp
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
catch_sgroups.cpp
Addresses #4434 (#4435)
2021-08-24 05:10:06 +02:00
Chirality.cpp
AssignStereochemistry should remove nonchiral atoms from StereoGroups (#4986)
2022-02-08 05:17:34 +01:00
Chirality.h
AssignStereochemistry should remove nonchiral atoms from StereoGroups (#4986)
2022-02-08 05:17:34 +01:00
CMakeLists.txt
Implemented a quick fix for issue 4875 (#4876)
2022-01-14 14:05:00 +01:00
Conformer.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
Conformer.h
operator= returns *this. (#5013)
2022-02-16 15:06:02 +01:00
ConjugHybrid.cpp
Stop trying to assign hybridization to actinides (#3281)
2020-07-25 05:04:54 +02:00
cptest.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
details.h
Change boost int types to std types (#2233)
2019-01-22 17:45:03 +01:00
FindRings.cpp
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
FindStereo.cpp
Fix some problems with perception of ring chirality in spiro-linked systems (#4280)
2021-07-02 14:14:02 -04:00
GraphMol.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
GraphMol.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
hanoitest.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
itertest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
Kekulize.cpp
Remove extra newline from Kekulize error message. (#5022)
2022-02-22 04:48:14 +01:00
Matrices.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
memtest1.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
MolBundle.h
miscellaneous updates (#4284)
2021-07-13 06:57:29 +02:00
MolOps.cpp
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
MolOps.h
Fixes #4789 (#4790)
2021-12-13 14:15:26 +01:00
molopstest.cpp
Fixes #4721 (#4722)
2022-01-28 16:38:46 +01:00
MolPickler.cpp
Fix some problems turned up by ossfuzz (#4927)
2022-01-22 04:30:06 +01:00
MolPickler.h
a few doxygen comment fixes (#4368)
2021-08-09 04:58:01 +02:00
MonomerInfo.cpp
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
MonomerInfo.h
Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)
2021-09-28 13:40:43 -04:00
new_canon.cpp
add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573)
2021-10-02 07:28:24 +02:00
new_canon.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
PeriodicTable.cpp
Fixes #3646 (#3653)
2020-12-17 08:34:15 -05:00
PeriodicTable.h
Run clang-format against header files (#4143)
2021-06-08 07:57:51 +02:00
QueryAtom.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
QueryAtom.h
Start adding move constructors and move-assignment operators (#4909)
2022-02-09 14:20:49 +01:00
QueryBond.cpp
Fixes github #4311 (#4312)
2021-07-09 15:06:54 +02:00
QueryBond.h
Start adding move constructors and move-assignment operators (#4909)
2022-02-09 14:20:49 +01:00
QueryOps.cpp
queries containing AtomAnd should not be considered atom lists (fixes #5006) (#5007)
2022-02-14 04:58:27 +01:00
QueryOps.h
fix warning (#4555)
2021-09-25 15:46:48 +02:00
querytest.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
RDKitBase.h
Enhanced stereo read/write support in SDF files. (#2022)
2018-09-26 15:44:23 +02:00
RDKitQueries.h
Fixes #1903 (#1971)
2018-07-25 09:14:17 +02:00
regress.txt
Unset executable flag
2019-10-10 20:18:43 +09:00
Renumber.cpp
Fix #4071 (#4080)
2021-04-23 16:45:54 -04:00
resMolSupplierTest.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Resonance.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
Resonance.h
- fixed #3349 (#3354)
2020-09-02 04:51:20 +02:00
RingInfo.cpp
Fixes #4721 (#4722)
2022-01-28 16:38:46 +01:00
RingInfo.h
Start adding move constructors and move-assignment operators (#4909)
2022-02-09 14:20:49 +01:00
Rings.h
Fix typo (#2862)
2019-12-31 06:43:27 +01:00
ROMol.cpp
Fixes #4127 (#4129)
2021-05-18 15:39:15 +02:00
ROMol.h
Start adding move constructors and move-assignment operators (#4909)
2022-02-09 14:20:49 +01:00
RWMol.cpp
Fix memory safety issues found by OSS-Fuzz (#4983)
2022-02-06 05:06:38 +01:00
RWMol.h
Start adding move constructors and move-assignment operators (#4909)
2022-02-09 14:20:49 +01:00
SanitException.h
Run clang-tidy (modernize-use-override) (#4251)
2021-07-01 05:18:56 +02:00
sanitTest.cpp
Modernize deprecated header inclusion (#3137)
2020-05-04 10:40:57 +02:00
StereoGroup.cpp
lambda cleanup (#4432)
2021-08-24 10:29:31 -04:00
StereoGroup.h
Start adding move constructors and move-assignment operators (#4909)
2022-02-09 14:20:49 +01:00
SubstanceGroup.cpp
lambda cleanup (#4432)
2021-08-24 10:29:31 -04:00
SubstanceGroup.h
Start adding move constructors and move-assignment operators (#4909)
2022-02-09 14:20:49 +01:00
test1.cpp
Fixes a couple of query-related bugs (#3398)
2020-09-17 08:16:43 +02:00
test-valgrind.cpp
run clang-tidy with readability-braces-around-statements (#2899)
2020-01-25 14:19:32 +01:00
testChirality.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
testMolBundle.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPickler.cpp
Improve test coverage and some bug fixes (#4536)
2021-09-26 07:45:06 +02:00
testPicklerGlobalSettings.cpp
Run clang-format against cpp (#4358)
2021-10-20 04:25:27 +02:00
testSGroup.cpp
Fixes #4468 and #4476 (#4482)
2021-09-05 05:43:13 +02:00
UnitTestQueryMol.py
Remove a bunch of Python2-related warts (#2315)
2019-03-06 20:43:49 -05:00